X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.37 α = 90
b = 47.37 β = 90
c = 104.54 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 125
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC COLLIMATOR 1997-05-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.73 25 97.2 0.068 6.8 -- 2.9 -- 16782 -- 0.0 40.3
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.73 1.86 95.7 0.225 22.5 3.7 2.8 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 1.73 10.0 -- 2.0 -- 13222 1339 89.9 -- -- 0.229 0.238 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.73 1.79 -- 967 112 0.33 0.358 0.031 74.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 53.7
Anisotropic B[1][1] -1.23
Anisotropic B[1][2] -3.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.46
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.59
x_bond_d 0.006
x_angle_deg 1.1
x_scangle_it 11.1
x_scbond_it 7.23
x_dihedral_angle_d 20.5
x_mcangle_it 6.62
x_mcbond_it 4.29
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1148
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 158

Software

Software
Software Name Purpose
SOLVE phasing
X-PLOR model building
CCP4 model building
X-PLOR refinement version: 3.851
UCSD data reduction
UCSD data scaling
X-PLOR phasing
CCP4 phasing